sisl.io.openmx.omxSileOpenMX
- class sisl.io.openmx.omxSileOpenMX(filename, *args, **kwargs)[source]
Bases:
SileOpenMX
OpenMX-input file
By supplying base you can reference files in other directories. By default the
base
is the directory given in the file name.- Parameters:
Examples
>>> omx = omxSileOpenMX("tmp/input.dat") # reads output files in 'tmp/' folder >>> omx = omxSileOpenMX("tmp/input.dat", base=".") # reads output files in './' folder
When using this file in conjunction with the sgeom script while your input data-files are named
input.dat
, please do this:sgeom input.dat{omx} output.xyz
which forces the use of the omx file.
Plotting
Plotting functions for the
omxSileOpenMX
class.plot.geometry
([output, ...])Calls
read_geometry
and creates aGeometryPlot
from its output.Methods
base_directory
([relative_to])Retrieve the base directory of the file, relative to the path relative_to
close
()dir_file
([filename, filename_base])File of the current Sile
get
(key[, default])Retrieve keyword from the file
read
(*args, **kwargs)Generic read method which should be overloaded in child-classes
read_basis
(*args, **kwargs)Reads basis
read_geometry
([output])Returns Geometry object
read_lattice
([output])Reads lattice
type
(label)Return the type of the fdf-keyword
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
Attributes
File of the current Sile
Return the current file name (without the directory prefix)
- base_directory(relative_to='.')
Retrieve the base directory of the file, relative to the path relative_to
- close()
- dir_file(filename=None, filename_base='')
File of the current Sile
- get(key, default=None)[source]
Retrieve keyword from the file
- Parameters:
key (
str
) – the key to search fordefault (optional) – if the key is not found, this will be the returned value (default to
None
)
- Returns:
value (
the value
ofthe key. If the key is a block
,a `list
is returned`,for
) – a real value a float (or if the default is of float), for an integer, an int is returned.
- plot.geometry(output: bool = False, *args, data_kwargs={}, axes: Axes = ['x', 'y', 'z'], atoms: AtomsIndex = None, atoms_style: Sequence[AtomsStyleSpec] = [], atoms_scale: float = 1.0, atoms_colorscale: Colorscale | None = None, drawing_mode: Literal['scatter', 'balls', None] = None, bind_bonds_to_ats: bool = True, points_per_bond: int = 20, bonds_style: StyleSpec = {}, bonds_scale: float = 1.0, bonds_colorscale: Colorscale | None = None, show_atoms: bool = True, show_bonds: bool = True, show_cell: Literal['box', 'axes', False] = 'box', cell_style: StyleSpec = {}, nsc: tuple[int, int, int] = (1, 1, 1), atoms_ndim_scale: tuple[float, float, float] = (16, 16, 1), bonds_ndim_scale: tuple[float, float, float] = (1, 1, 10), dataaxis_1d: np.ndarray | Callable | None = None, arrows: Sequence[AtomArrowSpec] = (), backend='plotly') GeometryPlot
Calls
read_geometry
and creates aGeometryPlot
from its output.- Parameters:
output – whether to read geometry from output files (default to read from the input file).
order (
{'dat', 'omx'}
) – the order of which to try and read the geometry. If order is present output is disregarded.axes – The axes to project the geometry to.
atoms – The atoms to plot. If None, all atoms are plotted.
atoms_style – List of style specifications for the atoms. See the showcase notebooks for examples.
atoms_scale – Scaling factor for the size of all atoms.
atoms_colorscale – Colorscale to use for the atoms in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
drawing_mode – The method used to draw the atoms.
bind_bonds_to_ats – Whether to display only bonds between atoms that are being displayed.
points_per_bond – When the points are drawn using points instead of lines (e.g. in some frameworks to draw multicolor bonds), the number of points used per bond.
bonds_style – Style specification for the bonds. See the showcase notebooks for examples.
bonds_scale – Scaling factor for the width of all bonds.
bonds_colorscale – Colorscale to use for the bonds in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
show_atoms – Whether to display the atoms.
show_bonds – Whether to display the bonds.
show_cell – Mode to display the cell. If False, the cell is not displayed.
cell_style – Style specification for the cell. See the showcase notebooks for examples.
nsc – Number of unit cells to display in each direction.
atoms_ndim_scale – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).
bonds_ndim_scale – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).
dataaxis_1d – Only meaningful for 1D plots. The data to plot on the Y axis.
arrows – List of arrow specifications to display. See the showcase notebooks for examples.
backend – The backend to use to generate the figure.
See also
GeometryPlot
The plot class used to generate the plot.
read_geometry
The method called to get the data.
- read(*args, **kwargs)
Generic read method which should be overloaded in child-classes
- Parameters:
kwargs – keyword arguments will try and search for the attribute
read_<>
and call it with the remaining**kwargs
as arguments.
- read_basis(*args, **kwargs)[source]
Reads basis
- Parameters:
output (
bool
, optional) – whether to read lattice from output files (default to read from the input file).order (
{'dat', 'omx'}
) – the order of which to try and read the lattice If order is present output is disregarded.
- read_geometry(output: bool = False, *args, **kwargs) Geometry [source]
Returns Geometry object
One can limit the tried files to only one file by passing only a single file ending.
- Parameters:
output – whether to read geometry from output files (default to read from the input file).
order (
{'dat', 'omx'}
) – the order of which to try and read the geometry. If order is present output is disregarded.
- read_lattice(output: bool = False, *args, **kwargs) Lattice [source]
Reads lattice
One can limit the tried files to only one file by passing only a single file ending.
- Parameters:
output – whether to read lattice from output files (default to read from the input file).
order (
{'dat', 'omx'}
) – the order of which to try and read the lattice. If order is present output is disregarded.
- type(label)[source]
Return the type of the fdf-keyword
- Parameters:
label (
str
) – the label to look-up
- write(*args, **kwargs)
Generic write method which should be overloaded in child-classes
- Parameters:
**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining
**kwargs
as arguments.
- property base_file
File of the current Sile
- property file
Return the current file name (without the directory prefix)
- plot
Plotting functions for the
omxSileOpenMX
class.